Suport from UNAM-PAPIIT Proyect "Formal Languages in Systems Biology" (PAPIIT is the program for suport to research and techonogical inovation of the National University of Mexico).

Computing lab facilities from the School of Science and the Applied Mathematics Institute at UNAM, including standard software and internet connections, as well as several seminar and classrooms for meetings.

We have RAISED OUR FUNDS TO cover for the registration of the team and individual members, as well as travel and local expenses for the instructors for the May meeting and approximately 60% of the corresponding costs for the students corresponding to the November meeting.

Some of the instructors are willing to devote part of their grants to support the IPN-UNAM iGEM team.

We have a grant from a current project which will allow us to cover the initial expenses. In the meantime, we have submitted another grant proposal specifically for iGEM. This proposal is likely to be accepted
within the next three months.

The Team Members:

14 members:

6 biology students

1 biomedical student

1 mathematics student

Introduction

One of the most important problems in developmental biology is the understanding of how structures emerge in living systems. Several mechanisms have been proposed, depending on the observed patterns. The so called Turing patterns are based on the interaction of two effects: diffusion of some chemicals, called morphogenes, and the chemical interaction between them. It has been highly controversial whether some patterns observed in several organisms are of this type. In particular, although some systems have been identified to be of activator-inhibitor type (the most popular Turing system proposed by Gierer and Meindhart), it is still questioned if pattern formation and more generally, the appearance of functional structures can be understood by means of Turing patterns or more broadly, reaction-diffusion mechanims.
One of the main goals of our project is to test different pattern formation mechanisms, not only Turing patterns, but also oscillatory and time varying structures. We propose that if the appropriate genetic construction is implanted in a colony of bacteria, the reaction-diffusion mechanism can be replaced by a genetic control system. This fact is first illustrated with the, by now classical, repressilator. Then we give two constructions of our own. The first is a modification of Elowitz system, which inclueded bot positive and inhibitory interactions. The positive ones are in fact dependent on quorum diffusible signals.

In order to model these systems, we use both a stochastic pi calculus and differential equations approach. For this construction experiments are yet to be performed.
For the other construction, we have two plasmids embedded in two different colonies. Each plasmid allows the bacterium to fluoresce red or green respectively.
Our hypothesis is that competition between these two colonies once they are allowed to
interact might function as a Turing system. For this we already have experimental results, and preliminary models.